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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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Install version 2.27 from source on Mac #945

Open VJalili opened 3 years ago

VJalili commented 3 years ago

I would need to install bedtools version 2.27.0 on macOS Big Sur 11.5.2. I take the steps as described in the documentation to build it from source, but the build fails with the following error messages:

$ wget https://github.com/arq5x/bedtools2/releases/download/v2.27.0/bedtools-2.27.0.tar.gz
$ tar -zxvf bedtools-2.27.0.tar.gz 
$ cd bedtools2/
# make
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.27.0
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/FileRecordTools
  * compiling FileRecordMgr.cpp
  * compiling FileRecordMergeMgr.cpp
- Building in FileReaders
  * compiling FileReader.cpp
In file included from FileReader.cpp:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:639:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^

... # more similar error messages, then:

fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [../../../../obj//FileReader.o] Error 1
make[1]: *** [FileReaders] Error 2
make: *** [src/utils/FileRecordTools] Error 2
Aleksandr-biochem commented 2 years ago

I have faced this problem too. At the end I have downloaded bedtools with conda: https://anaconda.org/bioconda/bedtools To my knowledge, that's the easiest way to set it up on mac os Big Sur or Catalina